Plastid directed DNA constructs comprising chimeric plastid targeting regions, vectors containing same and methods of use thereof

ABSTRACT

This invention relates to methods and compositions for obtaining  Arabidopsis  and  Brassica  plants. Specifically, the method provides culturing protocols and compositions that facilitate the regeneration of transformed plants following delivery of beneficial DNA molecules.

This application is a continuation of U.S. application Ser. No. 09/524,087, filed Mar. 13, 2000, now abandoned, which is a continuation-in-part of application Ser. No. 09/142,114, filed Feb. 5, 1999, now U.S. Pat. No. 6,376,744, which is a §371 of PCT/US97/03444 filed Mar. 6, 1997, which claims priority to provisional application No. 60/012,916, filed Mar. 6, 1996.

Pursuant to 35 U.S.C. Section 202(c), it is acknowledged that the United States government has certain rights in the invention describe herein, which was made in part with funds from the National Science Foundation Grant Number, MCB 93-05037.

FIELD OF THE INVENTION

The present invention relates to the field of transgenic plants. Specifically, the invention provides compositions and methods for the transformation of plastids in plants from the Cruciferae family.

BACKGROUND OF THE INVENTION

Several publications are parenthetically referenced in this application in order to more fully describe the state of the art to which this invention pertains. Full citations for these references are found at the end of the specification. The disclosure of each of these publications is incorporated by reference in the present specification as though set forth herein in full.

The plastid genome of higher plants is a circular double-stranded DNA molecule of 120-160 kb which may be present in 1,900-50,000 copies per leaf cell (Palmer, 1991; Bendich, 1987). Stable transformation of the tobacco plastid genome (plastome) has been achieved through the following steps: (i) introduction of transforming DNA, encoding antibiotic resistance, by the biolistic process (Svab et al. 1990a; Svab and Maliga 1993) or PEG treatment (Golds et al. 1993; O'Neill et al., 1993), (ii) integration of the transforming DNA by two homologous recombination events and (iii) selective elimination of the wild-type genome copies during repeated cell divisions on a selective medium. Spectinomycin resistance has been used as a selective marker encoded either in mutant plastid 16S ribosomal RNA genes Svab et al. 1990a; Staub and Maliga 1992; Golds et al. 1993), or conferred by the expression of an engineered bacterial aadA gene (Svab and Maliga 1993). Vectors which utilize aadA as a selectable marker gene and target the insertion of chimeric genes into the repeated region of tobacco plastid genome are available (Zoubenko et al., 1994). Selection of plastid transformants by kanamycin resistance, based on the expression of neomycin phosphotransferase (kan gene), is more difficult but also feasible (Carrer et al. 1993; Carrer and Maliga, 1995).

Transplastomic plants from agriculturally and pharmaceutically important species other than tobacco, are highly desirable. Expression of foreign genes of interest in the plastids of higher plants in the family Cruciferae provides several advantages over nuclear expression of foreign genes. These are 1) expression of exogenous DNA sequences in plastids eliminates the possibility of pollen transmission of transforming DNA; 2) high levels of protein expression are attainable; 3) the simultaneous expression of multiple genes as a polycistronic unit is feasible and 4) positional effects and gene silencing which may result following nuclear transformation are also eliminated.

SUMMARY OF THE INVENTION

The present invention provides improved methods for the generation of stably transformed, transplastomic plants. In one embodiment of the invention, cotyledon cells are cultured in high auxin liquid medium for a sufficient time period to stimulate uniform cell division. Initial culture is at a high density (50-200 cotyledons/20 ml). The cotyledons are then transferred to agar-solidified medium for delivery of exogenous, transforming DNA. Following delivery of transforming DNA, the cotyledons are transferred at a lower density (25-30/50 ml) to a medium containing high cytokinin levels and the selection agent to facilitate selection of transformants and plant regeneration. Presence of the exogenous DNA in the plastid genome is then confirmed by Southern blot analysis or PCR.

The transforming DNA molecules of the invention have several distinct features. These are 1) targeting segments flanking the foreign gene of interest may consist of plastid DNA sequences from the plant to be transformed, thereby facilitating homologous recombination of the transforming DNA into a predetermined region of the plastid genome or they may be chimeric in that they are derived from different species but possess partial homology that is sufficient to target insertion of transforming nucleic acid; 2) a selectable marker gene disposed within the targeting segment, conferring resistance to a selection agent; 3) 5′ and 3′ regulatory sequences derived from plastid DNA operably linked to sequences encoding a foreign gene of interest thereby enhancing expression of the transforming DNA and stability of encoded mRNA; and 4) at least one cloning site adjacent to the selectable marker gene for insertion of the foreign gene of interest which by itself is not selectable. Since the selectable marker gene and the foreign gene of interest form a heterologous block of contiguous sequence, integration of both genes into the plasid genome is effected.

In another embodiment of the invention, leaf cells are initially treated with high auxin media, followed by transformation with the transforming DNA and culturing in the presence of high cytokinin levels and a predetermined selection agent. Cells containing transformed plastids are maintained in the presence of the selection agent facilitating the obtention of homoplasmic cells which can then be regenerated into transplastomic plants.

In a further embodiment of the invention, tissue segments are directly placed on selective regeneration medium following bombardment.

In yet a further embodiment of the invention, an improved vector is provided which facilitates the generation of transplastomic plants. The improved vector comprises a targeting segment having first and second targeting sequences for facilitating recombination within the plastid genome, each of said first and second targeting sequences flanking at least one transgene of interest, at least one of said first and second targeting sequence being chimeric, said chimeric targeting sequence(s) having a first portion derived from the plant species targeted for transformation, and a second portion derived from a different plant species. Either the first, second or both targeting segments may be chimeric. In one embodiment the transgene comprises a selectable marker gene. In a preferred embodiment, the transgene comprises a polycistronic expression unit encoding both a selectable marker gene and a foreign gene of interest. Foreign genes of interest include without limitation, herbicide resistance genes, Bt genes, drought resistance genes, and other agriculturally and pharmaceutically beneficial protein encoding genes. Suitable selectable marker genes, include but are not limited to, those which confer resistance to kanamycin, streptomycin, and spectinomycin.

In yet another embodiment, transformed plant cells comprising the improved vectors of the invention are provided. Transformed plant cells include without limitation, cotyledon cells, leaf cells, hypocotyls and root cells. Transgenic plants comprising the improved vectors of the invention are also within the scope of the present claims.

Thus, the present invention provides novel methods and compositions for creating transplastomic plants. The genus Arabidopsis belongs to the mustard or crucifer family (Brassicaceae or Cruciferae), a widely distributed family of approximately 340 genera and 3350 species. The family is of significant economic importance as a source of vegetable crops, oil seeds, spices and, to a lesser extent, ornamentals. Much of its agricultural importance derives from the genus Brassica. Examples for Brassica ssp. of economic importance are: Brassica napus (oil seed), Brassica juncea (oil seed), Brassica campestris (oil seed), Brassica oleracea (broccoli, cauliflower, cabbage) Brassica nigra (black mustard) and Brassica hirta (white mustard).

Plastid transformation in Arabidopsis thaliana a model species for plant research (Meyerowitz and Sommerville, 1994) and Brassica ssp., an important agricultural crop is exemplified herein. These vectors and methods are suitable for transformation of plastids in other plants from the Cruciferae family.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic drawing illustrating the integration of aadA into the Arabidopsis plastid genome (ptDNA) after transformation with plasmid pGS31A. FIG. 1A shows a map of the transformation vector pGS31A, the ptDNA region containing the integrated spectinomcycin resistance (aadA) gene (T-ptDNA) and the cognate region of the wild-type ptDNA. 16SrDNA, rps12/7 and trnV are plastid genes (Shinozaki et al., 1986). FIG. 1B shows the regions of ptDNA contained in the Pi and P2 probes. FIG. 1C is an autoradiogram showing the results of Southern blot hybridization confirming integration of aadA in the plastid genome. The P1 targeting sequences hybridize to a 2.72-kb fragment in the wild-type (At) plants and to a larger, 3.82-k)b fragment in the transplastomic line (At-pGS31A-16). Note absence of wild-type fragment in transplastomic line. The aadA probe, P2, hybridizes only to the larger transplastomic fragment.

FIG. 2 is a schematic diagram of the plastid transformation protocol used for Arabidopsis leaves.

FIG. 3 is a schematic diagram of the different protocols used for obtaining fertile Arabidopsis plants from cotyledonary explants of Arabidopsis thaliana (RLD) having transformed plastids.

FIG. 4 is a map of the plastid targeting region of pGS7 and pGS85A plasmids. Note unique HincII cloning site in plasmid pGS7 and KpnI restriction site in plasmid pGS85, and chimeric kan kanamycin resistance gene. The plastid genes trnV, 16SrDNA and rps12/7 are described in Shinozaki et al., 1986. Site and direction of transcription initiation is indicated by horizontal arrow.

FIG. 5 is a sequence of the targeting region (SEQ ID NO: 1) of plasmid pGS7. The genes conferring resistance to kanamycin or spectinomycin will be inserted into the marked Hinc II site.

FIG. 6 is a sequence of the plastid targeting region (SEQ ID NO: 2) of plasmid pGS31A.

FIG. 7 is the sequence of the plastid targeting region (SEQ ID NO: 3) of plasmid pGS85A.

FIG. 8 is a schematic diagram showing the integration of foreign DNA into the Lesquerella fendleri plastid genome. FIG. 8A, Maps of cognate regions in the tobacco (Nt wt) and Arabidopsis (At wt) plastid genomes, and the plastid targeting region of vector pZS344. FIG. 8B, Integration of aadA16gfp into the Lesquerella plastid genome. Maps are shown for the plastid targeting region of vector pZS391B, the cognate region in the wild-type Lesquerella plastid genome (Lf wt) and transplastomic clones Lf-pZS391B-1 and Lf-pZS391B-2. FIG. 8C, DNA gel blots to test integration of vector sequences in the transplastomic clones. Blots were probed for: P1, aadA (NcoI-XbaI fragment; FIG. 8B); P2, HindIII-EcoRI targeting region fragment (FIG. 8A); P3, EcoRI-HincII targeting region fragment (FIG. 8A). Abbeviations: rrn16, 16S rRNA gene (Shinozaki et al. 1986).

FIG. 9 depicts transplastomic Lesquerella fendleri. FIG. 9A, Selection for spectinomycin resistance in bombarded leaf culture. Arrows point to resistant shoot and callus. FIG. 9B, Identification of transplastomic clones by resistance to streptomycin (200 mg L⁻¹) and spectinomycin (200 mg L⁻¹). Note one resistant (green) and two sensitive (yellow) clones. FIG. 9C, Grafted transplastomic plant in greenhouse. FIG. 9D, Testing resistance in seed progeny from cross Lf-pZS391-1D (maternal parent) and Lf-Spc5 (pollen parent; on left). Wild-type sensitive seedlings are shown on the right. Seeds have been germinated on 100 mg L⁻¹ spectinomycin.

FIG. 10 shows the localization of the spectinomycin resistance mutation to the plastid rrn16 gene by loss of an AatII restriction site. FIG. 10A, Map of the region containing the AatII site. Spectinomycin resistance mutation eliminates the AatII site. FIG. 10B, BamHI-AatII digested DNA was probed with the EcoRI-HincII fragment (P3 probe, FIG. 8A).

FIGS. 11A-D shows the nucleic acid sequence of the plastid targeting region (SEQ ID NO: 4) of pZS391b.

DETAILED DESCRIPTION OF THE INVENTION

A protocol for the transformation of plastids in Arabidopsis thaliana and Brassica napus has now been developed and the methods utilized to create these transformants are set forth below. The use of Arabidopsis and Brassica in the following examples is meant to be illustrative of the methods of the invention. The methods disclosed herein may be adapted to other plants in the Cruciferae family.

The plastids of Arabidopsis thaliana have been transformed following biolistic delivery of transforming DNA into leaf cells on the surface of microscopic (1 μM) tungsten particles as described below in Example I. The transforming plasmid pGS31A, used for these experiments carries a spectinomycin resistance (aadA) gene flanked by plastid DNA sequences to target its insertion between trnV and the rps 12/7 operon. Integration of aadA by two homologous recombination events via the flanking ptDNA sequences and selective amplification of the transplastomes on spectinomycin medium yielded spectinomycin resistant cell lines. Regenerated plants were homoplasmic in that the plastid genome copies had been uniformly altered by the transforming DNA. The efficiency of plastid transformation was low, two in 201 bombarded leaf samples. However, none of the 98 plants regenerated from the two lines were fertile.

These fertility problems were likely attributable to extended periods of treatment with 2,4-D, an auxin (Van der Graaff and Hooykas, 1996). It is possible that shortening exposure time to this agent may overcome the fertility problem. The relatively long growth period of Arabidopsis thaliana to provide a suitable source of leaves for transformation also makes leaves a less desirable tissue source.

Cotyledons and leaves each contain an abundant number of plastid genome copies per cell. Additionally, cotyledons provide a more available tissue source. Accordingly, cotyledon cells have been utilized as recipients for transforming DNA as set forth in Example II below. Cotyledon cells are preferred over leaf cells for practicing the methods of the present invention due to the relatively short (7 days) culturing period to prepare the cells for bombardment with transforming DNA. Another advantage to using cotyledon cells as the target cell is the reported regeneration of fertile Arabidopsis plants from immature cotyledons in the absence of 2,4-D (Patton and Meinke, 1988). In addition, protocols have been described for the regeneration of fertile Arabidopsis plants from leaf explants, also in the absence of 2,4-D (Lloyd et al., 1986; Van der Graaff and Hooykas, 1996).

As described in Example III, Arabidopsis thaliana and Brassica napus belong to the same family, Cruciferae, and therefore the plastid genomes share a high degree of homology and the gene order is essentially identical (Palmer et al., 1994). Accordingly, plastid transformation vectors and expression cassettes developed for Arabidopsis can be used for plastid transformation and expression of foreign genes in Brassica species without modification. The following definitions are provided to facilitate an understanding of the present invention:

-   Heteroplasmic: refers to the presence of a mixed population of     different plastid genomes within a single plastid or in a population     of plastids contained in plant cells or tissues. -   Homoplasmic: refers to a pure population of plastid genomes, either     within a plastid or within a population contained in plant cells and     tissues. Homoplasmic plastids, cells or tissues are genetically     stable because they contain only one type of plastid genome. Hence,     they remain homoplasmic even after the selection pressure has been     removed, and selfed progeny are also homoplasmic. For purposes of     the present invention, heteroplasmic populations of genomes that are     functionally homoplasmic (i.e., contain only minor populations of     wild-type DNA or, transformed genomes with sequence variations) may     be referred to herein as “functionally homoplasmic” or     “substantially homoplasmic. These types of cells or tissues can be     readily purified to homoplasmy by continued selection on the     selection medium. Most seed progeny of such plants are homoplasmic     in the absence of selection pressure, due to random sorting of     plastid genomes. -   Chimeric: a nucleic acid molecule having sequences derived from     different species. -   Transgene: a nucleic acid molecule encoding at least one foreign     gene of interest. Transgenes consisting of more than one coding     regions operably linked to appropriate expression signals may encode     one or more proteins. -   Plastome: the genome of a plastid. -   Transplastome: a transformed plastid genome. -   Transformation of plastids: stable integration of transforming DNA     into the plastid genome that is transmitted to the seed progeny of     plants containing the transformed plastids. -   Selectable marker: the term “selectable marker” refers to a     phenotype that identifies a successfully transformed organelle, cell     or tissue, when a gene or allele encoding the selectable marker is     included in the foreign DNA used for transformation. -   Transforming DNA: refers to homologous DNA, or heterologous DNA     flanked by homologous DNA, which when introduced into plastids     replaces part of the plastid genome by homologous recombination. -   Targeting segment: refers to those homogologous flanking regions     which facilitate homologous recombination between foreign DNA and     the plastid genome. -   Translationally fused: refers to two coding DNA segments within a     construct derived from different sources spliced together in a     construct such that a chimeric protein is expressed. -   High auxin culture medium: plant tissue culture medium which     contains auxin only, or a combination of high concentrations of     auxin and very low concentrations of cytokinins. The response of a     plant cell to an auxin is specific for a given taxonomic group. When     different auxins are applied in combination, their effects may not     be additive Furthermore, the tissue response to auxin may be     modified by cytokinins. Accordingly, the type and concentration of     auxin used should be determined empirically for the species to be     transformed. A preferred example of a high auxin medium for use in     the present invention is C1 medium, containing 1 mg/ml of the auxin     1-napthtaleneacetic acid (NAA) and a low concentration (0.2 mg/ml)     of the cytokinin 6-benzylaminopurine (BAP). Other auxins, such as     indole-3acetic acid (IAA) and dichloro-phenoxyacetic acid (2,4-D)     may also be used to stimulate uniform cell division. -   High cytokinin culture medium: like high auxin media, the response     of plant cells to high cytokinin media is taxonomic group specific.     An example of a preferred high cytokinin medium for use in the     present invention is C medium, containing 1 mg/L of BAP, 2 mg/l of     2iP, (6-(gamma,gamma-Dimethylallyamino)purine or IPA,     N6-(Isopentenyl)adenine) and a low concentration of the auxin NAA     (0.1 mg/L) other cytokinins which may be used is     6-Furfurylaminopurine (KIN or kinetin).

The detailed description provided in the following examples relates to preferred methods for making and using the DNA constructs of the present invention and for practicing the methods of the invention. Any molecular cloning and recombinant DNA techniques not specifically described are carried out by standard methods, as generally set forth, for example in Sambrook et al., “DNA Cloning, A Laboratory Manual,” Cold Spring Harbor Laboratory, 1989 or Ausubel et al. eds. in “Current Protocols in Molecular Biology”, John Wiley and Sons, 1995. Materials, methods and vectors suitable for transforming plastids are disclosed in U.S. Pat. Nos. 5,451,513 and 5,877,402, the entire disclosures of which are incorporated herein by reference.

The following examples are provided to more fully describe the instant invention. They are not intended to limit the scope of the invention in any way.

EXAMPLE I Plastid Transformation in Arabidopsis Leaves by Selection for Spectinomycin Resistance

The following materials and protocols enable the practice of the methods of Example I. A schematic diagram of the methods utilized is provided in FIG. 2.

Plant Material

As the recipient for transformation, the Arabidopsis ecotype RLD was used. This ecotype has been reported to regenerate readily in culture (Marton and Browse, 1991).

Construction of Vector pGS31A

The Arabidopsis plastid transformation vector pGS31A is shown in FIG. 1. The immediate progenitor of pGS31A is plasmid pGS7, a pBluescript KS(+) phagemid vector (Stratagene) derivative. Plasmid pGS7 carries a 2-kb HindIII-EcoRI Arabidopsis ptDNA fragment containing the 5′-end of the 16S rRNA gene, trnV and part of the rps12/7 operon. During construction of the pGS7 plasmid, the HindIII site has been removed by digestion with HindIII (site in 16SrDNA) and KpnI (in vector, treated with the T4 DNA polymerase to remove the single-stranded overhangs) and ligating the blunt ends. Vector pGS31A carries the selectable spectinomycin resistance gene, (Prrn::aadA::TpsbA) present in plasmid pZS197 (Svab and Maliga, 1993). The aadA coding region is transcribed from a synthetic promoter consisting of the promoter of the tobacco rRNA operon fused with a synthetic ribosome binding site (Prrn). The aadA mRNA is stabilized by transcriptionally fusing sequences downstream of the coding region with the 3′-untranslated region of the tobacco plastid psbA gene (TpsbA). The gene in pGS31A derives from a modified progenitor of pZS197 in which the XbaI site between aadA and TpsbA was removed by blunting. Plasmid pGS31A was obtained by excising the chimeric aadA gene with Ec1136II (an isochisomer of SacI, yields blunt ends) and BspHI (single-stranded overhang filled in to obtain blunt ends) for ligation into the unique HincII site of plasmid pGS7 between trnV and the rps12/7 operon. Tissue Culture Media

The tissue culture protocols were adapted from those of Marton and Browse (1991) and Czako et al. (1993). The Arabidopsis tissue culture media (ARM) is a derivative of the Murashige & Skoog (1962) MS medium. ARM medium: ms salts, 3% sucrose, 0.8% TC agar, 2 ml/L of the vitamin solution (100 mg myo-inositol, 5 mg vitamin B1, 0.5 mg vitamin B6, 0.5 mg nicotinic acid, 1 mg glycine and 0.05 mg biotin per ml). ARM1 medium: ARM medium containing 3 mg indoleacetic acid (IAA), 0.15 mg 2,4-dichlorophenoxyacetic acid (2,4-D), 0.6 mg benzyladenine (BA) and 0.3 mg isopentenyladenine (IPA) per liter. ARMIIr medium: ARM medium supplemented with 0.2 mg/L naphthaleneacetic acid (NAA) and 0.4 mg/L IPA. Arabidopsis shoot induction (ASI-N1B1) medium: ARM medium supplemented with 1 mg/L NAA and 1 mg/L BAP. The Arabidopsis shoots were rooted on ARM medium. Arabidopsis seed culture (ARM5) medium: ARM medium supplemented with 5% sucrose. The stocks of plant hormones were filter sterilized, and added to media cooled to 45° C. after autoclaving. Selective media contained 500 mg/L spectinomycin HCl and/or streptomycin sulfate. The antibiotics (filter sterilized) were added to media cooled to 45° C. after autoclaving.

Cultivation of Arabidopsis Plants in Sterile Culture

For surface sterilization, seeds (25 mg) were treated with 1 ml of commercial bleach (5.25% sodium hypochlorite) in an Eppendorf tube for 5-7 minutes with occasional vortexing. The seeds along with the bleach were poured into a 15 ml conical centrifuge tube containing 10 ml 90% ethanol and incubated for 5-7 minutes. The ethanol-bleach mix was decanted, and the seeds were washed 4 times with 10 ml autoclaved deionized water and finally resuspended in sterile water (approximately 150 seeds/ml). The resulting seed suspension (2 ml) was poured into 10 cm deep (10 mm high) petri dishes containing 50 ml ARM5 medium. The seeds were spread evenly by swirling the suspension. The water was then removed from the plates by pipetting. The seeds germinated after a 10-15 day incubation at 24° C. during which the plates were illuminated for 8 hours using cool-white fluorescent tubes (2000 lux).

To grow plants with larger leaves, seedlings were individually transferred to ARM5 plates (10 plants per 10 cm petri dish) and illuminated for 8 hours with cool-white fluorescent bulbs (lux; 21° C. day and 18° C. night temperature). The thick, dark green leaves, 1 cm to 2 cm in size, were harvested for bombardment after 5-6 weeks.

Transformation and Selection of Spectinomycin Resistant Lines.

Leaves (approximately 1.5 to 30 mm in length) for plastid transformation were harvested from aseptically grown plants. To cover a circular area 4 to 5 cm in diameter, 12 to 18 leaves were placed on agar-solidified ARMI medium. The pGS31A vector DNA was introduced into leaf chloroplasts by the biolistic process, on the surface of microscopic (1 μm) tungsten particles using a helium-driven PDS1000 biolistic gun. Fresh leaves were bombarded at 450 psi (target placed at 9 cm, from rupture disk; position No. 3 from top in the biolistic gun). Leaves cultured for 4 days on ARMI medium were bombarded at 1100 psi (target placed at 12 cm from rupture disk; position No. 4 from top in the biolistic gun).

Leaf bombardment was performed in ARMI medium. Following bombardment, the leaves were incubated for two additional days in ARMI medium. After this time period, the leaves were stamped with a stack of razor blades to create a series of parallel incisions 1 mm apart. It has been observed previously that mechanical wounding is essential to induce uniform callus formation in the leaf blades. The stamped leaves were transferred onto the same medium (ARMI) containing spectinomycin (500 mg/ml) to facilitate preferential replication of plastids containing transformed ptDNA copies. The ARMI medium induces division of the leaf cells and formation of colorless, embryogenic callus. After 7-10 day selection on ARMI medium, spectinomycin selection was continued on the ARMIIr medium which normally induces greening. Since spectinomycin prevents greening of wild-type cells, only spectinomcyin-resistant cells formed green calli. Visible green cell clusters on the selective ARMIIr medium appeared within 21 to 70 days.

In 201 bombarded samples, 19 spectinomcyin-resistant lines were obtained. Plant regeneration was attempted in 14 spectinomycin-resistant lines, and succeeded in 10 of them. Shoots from the green calli regenerated on the ASI-N1B1 medium, and were rooted on ARM medium.

Table 1 sets forth the recovery of spectinomycin resistant cell lines after biolistic delivery of plasmid pGS31A.

TABLE 1 Recovery of spectinomcyin resistant lines after bombardment of A. thaliana with plasmid pGS31A Number of Number of Transgenic Spont. DNA¹ Samples psi2 Spc^(r) Plant pt Nucleus mutant. N/A 100 1 0 1 pGS31A 40 1100 8 6 1 7 0 pSG31A 151 450 11 8 1 10 0 ¹The control plates were not bombarded. ²psi = pounds per square inch, the value of rupture disk. Southern Hybridization Analysis of Total Cellular DNA to Verify Plastid Transformation

Spectinomycin resistance may be due to expression of aadA in plastids (Svab and Maliga, 1993), expression of aadA in the nucleus (Svab et al., 1990b), or spontaneous mutation (Fromm et al., 1987; Svab and Maliga, 1991). Southern hybridization was performed to identify plastid tranformants in the spectinomycin resistant lines isolated. Total cellular DNA was isolated according to Mettler (1987). Restriction enzyme-digested DNA was electrophoresed in 0.7% agarose gels and transferred to nylon membrane (Amersham) using the PosiBlot transfer apparatus (Stratagene). Blots were probed by using Rapid Hybridization Buffer (Amersham) with ³²P labeled probes generated by random priming (Boehringer-Mannheim). When using the targeting ptDNA as a probe, in lines At-pGS31A-2 and At-pGS31A-16, the 3.82 kb transgenic fragment was the only fragment detected indicating that the wild-type ptDNA copies have been selectively diluted out during cell divisions on the selective medium. The same transgenic fragment also hybridized with the aadA probe (FIG. 1C).

Among the 19 spectinomycin resistant lines, 17 nuclear transformants were identified by a wild-type fragment on Southern blots when hybridizing with the targeting ptDNA probe. Note that the Southern blots used were optimized for the high-copy (10,000 per cell) leaf ptDNA and will not give a signal with a few nuclear aadA copies.

Spontaneous mutants are expected to have wildtype ptDNA targeting fragment on Southern blots and no PCR-amplifiable aadA gene. In the sample of 19 spectinomycin resistant lines, no such spontaneous mutant was found.

PCR Amplification of Inserted aadA Sequences

DNA was amplified according to standard protocols (1 min at 92° C., 1.5 min at 58° C., 1.5 min at 72° C., 30 cycles). Spectinomycin resistance resulting from aadA expression may be verified by PCR amplification of a 407 nucleotide internal segment using the following primers: 5′-GCTTGATGAAACAACGCGG-3′ 5′-CCAAGCGATCTTCTTCTTGTCCAAG-3′

Transplastomic Arabidopsis Plants

While the transplastomic Arabidopsis plants all flowered, none of them set seed after selfing, or after fertilization with pollen from wild-type plants. Included among these were 98 plants regenerated from the two lines in which spectinomcyin resistance was due to plastid transformation, and 66 plants regenerated from 12 lines in which spectinomcyin resistance was due to expression of aadA in the nuclear genome.

Conclusions and Implications

An important agricultural breakthrough, plastid transformation in the model species Arabidopsis thaliana is described in the instant invention. Based on the foregoing results, it has been found that a chimeric aadA gene, when inserted in the Arabidopsis ptDNA targeting cassette, was suitable to recover plastid transformants following biolistic delivery of the transforming DNA. However, the number of Arabidopsis plastid transformants was significantly lower, about one in 100, than anticipated based on the transformation of tobacco plastids which yields on average one transformant per bombarded sample (Svab and Maliga, 1993; Zoubenko et al., 1994).

There may be multiple reasons for the relatively low transformation efficiency. Inherent species-specific differences, such as relatively inefficient homologous rb-combination system in Arabidopsis chloroplasts could be one obvious reason.

In tobacco vector pZS197, aadA is flanked by 1.56-kb and 1.29-kb of ptDNA, and yields approximately 1 transformant per bombardment (Svab et al., 1993). In plasmid pRB15, also a tobacco vector, aadA is flanked by larger targeting segments, 1.56-kb and 3.6-kb of ptDNA, and yields approximately 5 plastid transformants per bombardment (Bock and Maliga, 1995). In Arabidopsis vector pGS31A aadA is flanked only by approximately 1-kb plastid targeting sequence on both sides. Therefore, the efficiency of plastid transformation in Arabidopsis may be significantly improved by increasing the size of the targeting ptDNA fragment.

In contrast to tobacco, in which most of the plants regenerated from leaves are fertile, it was surprising to find that none of the 164 regenerated Arabidopsis plants set seed. Lack of fertility, in part, may be due to the extensive polyploidy of leaf tissue as reported by Galbright et al., (1991) and Melaragno et al. (1993). An additional reason for lack of fertility may be the prolonged exposure of the cultures to 2,4 D (Van der Graaff and Hooykaas, 1996).

EXAMPLE II Plastid Transformation in Arabidopsis Cotyledons by Selection for Kanamycin Resistance

Plastid transformation has been obtained in Arabidopsis thaliana by selection for spectinomycin resistance in leaf cultures following bombardment with DNA-coated tungsten particles, as set forth in Example I. While plastid transformation has been successful, the regenerated plants were not fertile. These obstacles have been overcome by altering certain parameters of the transformation protocol.

The protocol developed and set forth in this Example has the following salient features: (1) Cotyledons obtained by germinating mature seed are used to advantage because of their ready availability, and the ease by which large quantities of sterile cotyledons are obtained from surface-sterilized seed. (2) The protocol has two distinct steps. The first step employing a high auxin medium to induce uniform cell division throughout the cotyledon (Stage I) and the second step including a high cytokinin medium to induce plant regeneration (Stages II and III). The protocol was designed to either minimize exposure to medium containing 2,4-D during tissue culture, or more preferably to eliminate such exposure completely. (3) Initial culturing of the cotyledon cells at a high density, i.e., 500-200 cotyledons/20 ml in liquid culture medium during the first 8 days (Stage I, II) proved essential for obtaining abundant plant regeneration later.

The protocol for plastid transformation in Arabidopsis utilizing cotyledons as target tissue and kanamycin-resistance as a selective marker was implemented as follows. The chimeric kan gene derives from plasmid pTNH7, a pUC118 derivative encoding neomycin phosphotransferase (NPTII), an enzyme which enzymatically inactivates the kanamycin antibiotic. The same chimeric kan gene in a tobacco targeting plasmid (plasmids pTNH32) was used for direct selection of plastid transformants in tobacco (Carrer et al. 1993). The construction of the kan gene was described in more detail in this same reference. Plasmid pGS85A was obtained by excising kan from pTNH7 as a SacI/PstI fragment, blunting, and cloning the fragment into the HincII site of plasmid pGS7 (FIG. 4). The kan gene in pGS85A, as aadA in plasmid pGS31A, is expressed in a Prrn/TpsbA cassette. However, the five N-terminal amino acids of the highly-expressed rbcL coding region were translationally fused with the neomycin phosphotransferase-terminus. This translational fusion in tobacco lead to the accumulation of NPTII at 10× higher levels than from identical, constructs without the rbcL-terminal segment. The DNA sequence of pGS85A, including that of the chimeric kan gene, is set forth herein.

Initially, seed-set was tested in plants regenerated via the tissue culture protocol. Selection of kanamycin resistant clones after bombardment with DNA-coated tungsten was subsequently assessed. These improvements to the method are suitable for the generation of fertile, transformed Arabidopsis plants. The following material and protocols were utilized in practicing the methods of this Example II.

Seed Germination

Seeds of Arabidopsis thaliana ecotype RLD are surface sterilized using commercial bleach (5% sodium hypochlorite) for 5 minutes followed by a subsequent 5 minute treatment with 95% ethanol. A drop of Triton X-100 was added to the bleach to wet the surface of the seeds during the sterilization period. After sterilization, seeds were washed 5-6 times with sterile deionized water. Seeds were germinated on GM medium in 10 cm Petri dishes. See Table 2. The Petri dishes were incubated for 8 to 9 days in a Percival growth chamber at 23° C. under continous light.

TABLE 2 Composition of seed germination (GM) medium. Medium Concentration (mg/L) MS basal salts 0.5X myo-inositol 100 Thiamine 0.1 Pyridoxine 0.5 Nicotinic acid 0.5 Glycine 2.0 Sucrose 30 g/L pH 5.8 Reference: van der Graaff and Hooykaas, 1996. Tissue Culture Media and Culture Conditions

Compositions of the tissue culture media used for Stages I, II and III of the selection protocol are listed in Tables 2 and 3. Stage I and Stage II liquid cultures were established by aseptically transferring at least 50 to 2000 cotyledons to a Petri dish (100 mm×20 mm), each dish containing approximately 20 ml of medium. The Petri dishes were incubated at 23° C. on a New Brunswick G10 gyrotory shaker at 60 rpm and illuminated for 16 hours with cool fluorescent-light. In the Stage III protocol, cotyledons were incubated on agar-solidified (0.8% TC agar, JRH Biosciences) media at approximately 25-30 cotyledons per Petri dish (100 mm×20 mm) in 50 ml of media. The cultures were illuminated as described for Stages I and II.

Regenerated plants were directly transferred to GM medium in Magenta boxes with vented lids for gas exchange. Plants in the Magenta boxes were incubated in the culture room at 23° C., and illuminated for 16 hours with cool fluorescent light. The plants flowered and set seeds in the boxes.

The methods described for Example I were modified to generate fertile Arabidopsis plants having transformed plastid genomes. Three distinct tissue culture stages were employed to obtain plastid transformation. Stage I: liquid culture, in high auxin medium to stimulate uniform cell division. Stage II: liquid culture, in high cytokinin medium to induce plant regeneration from the transformed cells. Stage III: culture on agar-solidified medium, containing high levels of cytokinins also to induce plant regeneration.

A schematic diagram of the strategy used to identify the best protocol for obtaining fertile plastid transformants is outlined in FIG. 3. To induce uniform cell division in liquid culture, four media, C1 (van der Graaff and Hooykaas, 1996), ARM I (Marton and Browse, 1991), R3 and PG1 (Feldmann and Marks, 1986; reported to induce callus and/or somatic embryogenesis in Arabidopsis) were utilized. Stage I treatment was kept short (2 days) to adopt to the usual timing of transferring the explants to a selective medium after bombardment, and to minimize the adverse effect of 2-4-D, if used at all. The composition of the Stage I tissue culture media utilized is set forth in Table 3 below.

TABLE 3 Composition of stage I tissue culture media*. Media ARM I C1 R3 PGI Basal salts MS MS MS MS Vitamins ARM I B5 MS B5 2,4-D 0.15 — 0.5 2.2 BAP 0.6 0.2 — — IAA 3.0 — 5.0 — IPA 0.3 — — — NAA — 1.0 — — KIN — — 0.3 0.05 Sucrose 30 g 30 g 30 g 30 g pH 5.8 5.8 5.8 5.8 *All components are in mg/L. References: ARMI, Marton and Browse, 1991; C1, van der Graaff and Hooykaas, 1996; R3 and PG1, Feldmann and Marko (1986).

For Stage II culture, only one medium (A; Table 4) was used. This medium was efficient for inducing plant regeneration from immature cotyledons (Patton and Meinke, 1988). The cotyledons at Stage II were kept for a total of 6 additional days at high density in liquid culture.

For Stage III culture, the cotyledons were transferred to four types of agar-solidified regeneration media. These include the A medium developed for plant regeneration from immature embryos (Patton and Meinke, 1988); the B medium developed for plant regeneration from root explants (ARMII; Marton and Browse, 1991); the C medium that designed herein; and the D medium which is an embryo-induction medium for roots (ARMI; Marton and Browse, 1991) and leaf explants (Example I).

TABLE 4 Stage II and stage III plant regeneration media. Media A medium* B medium* C medium* D medium* Basal salts MS MS MS MS Vitamins B5 B5 B5 B5 NAA 0.1 — 0.1 — IAA — 0.1 — 3.0 BAP 1.0 — 1.0 0.6 2iP — 4.0 2.0 0.3 2,4-D — — — 0.15 Sucrose 30 g 30 g 30 g 30 g Agar (TC)  7 g  7 g  7 g  7 g pH 5.8 5.8 5.8 5.8 *All components are in mg/L. A medium is based on Patton and Heinke, 1988; B medium is the same as ARMII in Marton and Bowse, 1991; C medium developed herein, based on A and D media; D medium is the same as ARMI embryo-induction medium in Marton and Browse, 1991. Plant Regeneration and Testing of Fertility

Cotyledons remained green and slightly expanded in size during the first 2 days of culture at Stage I in all four media. After 2 days in callus/embryo induction medium, cotyledons for Stage II were transferred from all four media to the A liquid regeneration medium. Green callus started appearing after 3 days of culture in A medium and by the 7th day callus appeared all over the cotyledons. At this stage cultures were transferred to the semi-solid media of Stage III which promotes embryo/shoot growth. Calli derived from media 1 (ARM1) and 2 (C1) were green. Development of plantlets from these explants could be seen by 21 days of culture. Callus derived from media 3 (R3) and 4 (PG1) was also green but very compact. This is probably due to the high concentration of 2,4-D in the Stage I media. A few plantlets in these cultures appeared only after 30 days. Plants from all cultures were transferred to hormone free GM medium as soon as they were 5-10 mm in size.

The protocols diagrammed in FIG. 3 were evaluated at two levels: uniform induction of cell division and shoot regeneration from the cotyledons; and by production of viable seed on the regenerated plants. The results are summarized in Table 5. Based on the first criterion, the best combination was 2AC, that is C1 medium at Stage I and C medium at Stage III, these treatments resulted in prolific shoot regeneration which was observed on each of the explants. The second best combination was 1AC (35 out of 40 explants regenerating shoots), with ARM1 at Stage I and medium C at Stage III. Combinations with media 3 and 4 at Stage I performed very poorly, with only a very small fraction of cotyledons forming shoots.

As to formation of viable seed, with one exception each of the regenerated plants produced viable seed. See Table 5. Most importantly, no adverse effect on fertility was found in the two combinations (2AC and 1AC) in which shoot regeneration is prolific.

TABLE 5 Seed-set in Magenta boxes on Ara.bidopsis thaliana RLD plants regenerated via plastid transformation protocols schematically shown in FIG. 3. Number of Number of Number of Number of cotyledons cotyledons plants with viable Media cultured with shoots in boxes seed 1AA 40 20 8 8 1AB 40 25 8 8 1AC 40 35 8 8 1AD 40 — — — 2AA 40 25 12 12 2AB 40 22 8 7 2AC 40 40 16 16 2AD 40 2 — — 3AA 40 12 4 4 3AB 40 6 4 4 3AC 40 20 — — 3AD 40 1 — — 4AA 40 1 — — 4AB 40 1 — — 4AC 40 4 4 4 4AD 40 1 — 1 Selection of Plastid Transformants by Kanamycin Resistance

Expression of kan encoding neomycin phosphotrasferase (NPTII) confers resistance to kanamycin when introduced into the Arabidopsis nucleus. Engineered forms of kan have been extensively used to obtain nuclear transformants in Arabidopsis, see Valvekens et al., 1988, and Brassica, see Radke, et al., 1992. The kan gene has been converted into a plastid marker for the selection of plastid transformants in tobacco (Carrer et al., 1993). As set forth in Example I, Arabidopsis plastid transformants have been obtained by selection for spectinomycin resistance conferred by aadA in the tobacco Prrn/TpsbA cassette. Prrn is a promoter derived from the plastid rRNA operon and TpsbA contains the plastid psbA gene 3′ untranslated region required for the stabilization of chimeric plastid mRNAs (Svab and Maliga, 1993). A kanamycin resistance marker gene suitable for the selection of plastid transformants may be obtained by expressing kan in the Prrn/TpsbA cassette. A suitable kanamycin resistance plastid transformation vector from Arabidopsis and Brassica is the pGS85A vector which carries the chimeric kanamycin gene from plasmid pTNH32 (Carrer et al. 1993). The insertion site in pGS85A is the Hinc II site in the trnV/rps12/7 intergenic region. However, other intergenic regions in the plastid genome may be targeted as long as the introduced transgene does not interfere with the expression of the flanking plastid genes.

Plastid transformation may be carried out following the 1AC or 2AC tissue culture protocols outlined above. To prepare a suitable target tissue for transformation, cotyledons from 8-9 day old seedlings are cut from seedlings in liquid ARM and C1 media and cultured for two days as dictated by the 1AC and 2AC protocols (FIG. 3). After two days the cotyledons are transferred to filter paper (Whatman No. 4) on agar-solidified non-selective medium of identical composition. Approximately 50 to 70 cotyledons are required to cover a 3 CM² area. The cotyledons are then bombarded with plasmid pGS85A, a transforming, kanamycin resistance, Arabidopsis vector. Plasmid preparation, coating of tungsten particles and bombardment are carried out as described for tobacco (Maliga, 1995). For phenotypic expression, the cotyledons may be left in the same plates for two days. Subsequently, the cotyledons may be transferred to a selective liquid A medium containing 50 mg/L kanamycin sulfate and cultured for an additional seven days. After 7 days, cotyledons are transferred to a selective, agar-solidified C medium containing 50 mg/L kanamycin. In an alternative embodiment, selection may be carried out initially using kanamycin at 25 mg/ml. At later stages of culture, the kanamycin concentration is increased to 50 mg/ml. Callus growth from the transformed cells on the selective medium may be observed as early as one week. However, additional kanamycin-resistant clones may appear for several more weeks. Some of these are plastid transformants, while others acquire resistance to kanamycin due to the expression of the plastid kan gene in the nucleus (Carrer et al., 1993). The two classes of kanamycin-resistant clones can be readily distinguished DNA gel blot analysis and PCR analysis (as described in Example I). DNA was amplified according to standard protocols (1 min at 92° C., 1.5 min at 58° C., 1.5 min at 72° C., 30 cycles). Kanamycin resistance occurs as the result of neomycin phosphotransferase gene expression which may be verified by PCR amplification of a 548 nucleotide internal segment using the following primers: 5′-CCGACCTGTCCGGTGCCC-3′ 5′-CACGACGAGATCCTCGCCG-3′.

EXAMPLE III Plastid Transformation in Brassica napus Leaves by Selection for Resistance to Spectinomycin and Kanamycin

Given their essentially identical genomes, plastid transformation vectors and expression cassettes developed for Arabidopsis can be used to advantage for plastid transformation and expression of foreign genes in Brassica species without modification.

Certain plastid expression signals derived from evolutionarily distant species function in Arabidopsis and Brassica plastids. This observation is supported by the results described in Example I demonstrating that the tobacco Prrn/TpsbA cassette can be used for expressing the selectable spectinomycin resistance gene (aadA) in Arabidopsis plastids. However, not every tobacco expression signal functions properly in Arabidopsis. Studies with a vector identical to pGS31A, except that the termination signal TpsbA, has been replaced with signal Trps16 has a dramatic effect on obtaining plastid transformants. This plasmid gene was obtained by inserting the Prrn/Trps16 cassette into targeting site in the pGS7 vector. See FIG. 4. Zero plastid transformants were obtained out of 416 samples bombarded with this plasmid. As mentioned above, when a Prrn/TpsbA cassette (cassettes described in Staub and Maliga, Plant Journal 6: 547-553, 1994 and Svab and Maliga, 1993, the subject matter of which is incorporated herein by reference) was utilized to transform Arabidopsis leaves, plastid transformants were obtained, 2 out of 210 samples bombarded.

Due to their taxonomic relatedness, Arabidopsis and Brassica species respond similarly in tissue culture to plant hormones or to antibiotics. As a result, plant regeneration from cultured cells and selection of transgenic lines by antibiotic resistance may be accomplished by essentially the same protocol. Both Arabidopsis and Brassica leaf or cotyledon explants respond to 500 mg/L spectinomycin with prolific callus growth in wild-type, non-transformed tissue on shoot regeneration medium, such as medium C described in Table 6. This response differs significantly in tobacco leaf tissue wherein exposure to 500 mg/ml of spectinomycin results in a severe inhibition of callus proliferation on shoot induction medium. Thus, tobacco plastid (and nuclear gene) transformants can be readily regenerated on a shoot induction medium containing spectinomycin at 500 mg/L (Svab and Maligam 1993). Unfortunately, rapid callus proliferation on spectinomycin-containing C shoot/embryo regeneration medium (see table 6) prevents the recovery of Arabidopsis and Brassica plastid transformants. Culture conditions must be improved to suppress rapid callus growth to facilitate the recovery of plastid transformants. Such conditions are outlined in Example I. While selection was feasible and plastid transformants were obtained using the methods of Example I, the transplastomic plants generated were not fertile. However, given the higher tolerance of Brassica to 2,4 D (Radke et al., 1992) the same protocol described in example I may be adapted for use in Brassica.

The data presented in Example II indicate that kanamycin selection is compatible with the regeneration protocols described. Accordingly, kanamycin is the favored antibiotic for the selection of plastid transformants in the Cruciferae taxonomic group.

Examples I and II disclose protocols for the regeneration of transgenic plants from Arabidopsis leaves and cotyledons. A protocol for the regeneration of transgenic plants in Brassica would involve a two-stage protocol (application of two different media) for leaves, and a three-stage protocol (application of three different media) for cotyledons. The three-stage protocol described for use in the plastid transformation of Arabidopsis cotyledons in Example II is suitable for use in Brassica. Accordingly only the methods for transforming Brassica leaf plastids in a two stage process will be described below.

Plastid Transformation in Brassica Utilizing Leaves as Target Tissue and Kanamycin Resistance as the Selective Marker

Brassica Stage I culture results in the uniform induction of cell division in leaves or cotyledons. The objective of Stage II is regeneration of transgenic plants. A suitable Stage I medium for the induction of cell division would be the ARMI medium discussed in Examples I and II. Suitable Stage II regeneration media would be the B medium (ARMII in Marton and Browse, 1991), C medium (this study) and E medium (Pelletier et al. 1983) listed in Table 6.

TABLE 6 Stage II Brassica plant regeneration media* Media B medium C medium E medium Basal salts MS MS MS Vitamins B5 B5 B5 NAA — 0.1 1.0 IAA 0.1 — — BAP — 1.0 — 2iP 4.0 2.0 1.0 GA3 — — 0.02 Sucrose 30 g 30 g 30 g Agar (TC)  7 g  7 g  7 g pH 5.8 5.8 5.8 *All components are in mg/L. B medium is the same as ARMII in Marton and Bowse, 1991; C medium is this study; E medium is the cruciferae regeneration medium of Pelletier et al. 1983.

For selection of plastid transformants, Brassica napus cv. Westar seeds should be surface sterilized, and germinated aseptically in Magenta boxes as described for Arabidopsis in Example II. After three to four weeks, the leaves are harvested, and directly placed on a Whatman filter paper placed on agar-solidified non-selective Stage I medium. Following bombardment with DNA of the appropriate plastid transformation vector carrying a selectable kanamycin-resistance marker, as described in Example II, the plates are incubated for two days in the light (16 hours) at 25° C. After 2 days the leaves are incised with a stack of sterile razor blades, and transferred to the same Stage I medium supplemented with 50 mg/L of kanamycin sulfate. In an alternative embodiment, selection may be carried out initially using kanamycin at 25 mg/ml. At later stages of culture, the kanamycin concentration is increased to 50 mg/ml. After two weeks on the selective Stage I medium, the leaves are transferred to one of the Stage II media for plant regeneration. Kanamycin resistant clones are identified by their rapid growth and shoot regeneration on the selection medium. Kanamycin resistance may be due to plastid transformation or integration of the kanamycin marker gene into the nuclear genome. Plastid transformation is verified by PCR and DNA gel blot analysis in tissue samples taken from kanamycin-resistant calli and regenerating shoots. The regenerated shoots are then rooted and transferred to soil in the greenhouse following standard protocols.

Example IV Plastid Transformation in Lesquerella fendleri, an Oilseed Brassicacea

A plastid transformation protocol has also been developed in Lesquerella fendleri, a wild oilseed species of the Brassicaceae family with a high capacity for plant regeneration in tissue culture. Plastid transformation vector pZS391B carries a selectable spectinomcyin resistance (aadA16gfp) gene targeted for insertion in the trnV/rps12/7 intergenic region. Transforming DNA was introduced into Lesquerella leaves by the biolistic process. Spectinomycin prevented greening of non-transformed cells. Transplastomic clones were identified by their ability to form green shoots on the selective medium (400 mg/L spectinomcyin HCl). The transplastomic clones were also resistant to streptomycin, a characteristic of clones expressing aadA. Selection in 51 bombarded samples yielded 2 transplastomic clones. Fertile plants and seed progeny were obtained in transplastomic clone Lf-pZS391B-1.

In the same samples, 108 spontaneous mutants were identified. Spontaneous mutants, unlike the transformed clones, were resistant only to spectinomycin. Spectinomcyin resistance in four of the spontaneous mutants was localized to the 16S rRNA gene by the loss of a conserved AatII site. High regeneration potential in tissue culture is believed to be important for efficient plastid transformation. Although Lesquerella has a high regeneration potential, we report here plastid transformation efficiencies similar to those in Arabidopsis, a species with poor morphogenetic capacity. Thus, it appears that competence for plastid transformation in the oilseed Brassicacea Lesquerella fendleri is not linked to regeneration capacity.

Plastid transformation in non-tobacco species is much less efficient than that reported in tobacco. It has been hypothesized, that lower plastid transformation efficiency could be due to inefficient regeneration of plants from cultured cells (Sidorov et al. 1999). Lesquerella fendleri is a plant with a desirable seed oil composition making it a candidate for commercial production. The capacity for plant regeneration from cultured cells of Lesquerella is comparable to the morphogenic response of tobacco (Skarzhinskaya et al. 1996).

Both Arabidopsis thaliana and Lesquerella fendleri belong to the mustard family (Brassicaceae). In accordance with the present invention, experiments have been performed to determine if the high morphogenetic potential in Lesquerella may be correlated with competence for plastid transformation. The data reveal that plastid transformation efficiency is similar in Lesquerella and Arabidopsis. Thus, competence for plastid transformation does not appear to be linked to regeneration potential, at least not in the oilseed Brassicacea Lesquerella fendleri.

The following materials and methods are provided to facilitate the practice of the present invention as described in Example IV.

Construction of Vector PZS391B

Plastid transformation vector pZS391B is a pUC119 plasmid derivative lacking a ScaI site in the flanking vector sequence and targets insertions into the trnV-rps12/7 intergenic region of the Lesquerella plastid genome. The plasmid is a modified version of the Arabidopsis plastid vector pGS31A shown in FIG. 1 (Sikdar et al. 1998). Part of the left targeting region containing the 16S rRNA gene derives from the tobacco plastid genome (EcoRI-SphI fragment, at nucleotides 138540 and 139818 in the tobacco plastid genome; GenBank Accession No. Z00044). The rest of the left targeting region derives from the Arabidopsis plastid genome (SphI-HincII fragment, at nucleotide positions 137590 and 138094 in the Arabidopsis plastid genome; GenBank Accession No. AP000423). The selectable marker gene aadA16gfp utilized in this example encodes aminoglycoside 3′-adenyltransferase translationally fused via a 16-mer linker with the Aequorea victoria green fluorescent protein (Khan and Maliga 1999). The aadA16gfp gene is expressed in an expression cassette consisting of a modified tobacco plastid rRNA operon promoter PrrnLrbcL (Kuroda and Maliga 2000) and the 3′ untranslated region of the plastid psbA gene (TpsbA)(Khan and Maliga 1999). The right targeting region is comprised of a HincII-XbaI Arabidopsis plastid DNA fragment (restriction sites at nucleotides 138094 and 138943; GenBank Accession No. AP000423). DNA sequence of plasmid pZS391B plastid targeting region has been deposited in GenBank (GenBank Accession No. not yet assigned). To obtain plasmid pZS391B, the chimeric aadA16gfp gene was cloned as an EcoRI-HindIII fragment into a BluescriptII KS+ vector, then excised as a SmaI-HincII fragment and ligated into HincII digested pZS344.

Plastid Transformation

Lesquerella fendleri (Gray) Wats seed (A 14581) was obtained from the USDA Western Regional Plant Introduction Station, Pullman, Wash. The plants were grown aseptically on hormone free C1 medium, which is a modified MS medium (Van der Graaff and Hooykaas 1996) at 24° C., and illuminated for 16 hours a day. Leaf segments (10 to 15 mm) were harvested from six-week old plants. For bombardment, 10 to 12 leaf segments were placed on a filter paper abaxial side up on C2 medium (C1 medium containing 1 mg L⁻¹ BA and 0.1 mg L⁻¹ NAA). Leaf segments were bombarded with tungsten particles (M−10; 0.6 to 0.9 μm) coated with pZS391B plasmid DNA (DuPont PDS1000He Biolistic gun; 1100 p.s.i.)(Maliga 1995). Two days after bombardment the leaves were cut into smaller pieces (5 mm long), dissected longitudinally to yield 2-mm wide strips and placed on C2 medium containing 400 mg L⁻¹ spectinomycin HCl. The leaf segments were subcultured to the same selective medium at 14 to 20 day intervals. Spectinomycin resistant clones appeared in 5 to 7 weeks, identified as green shoots on bleached sensitive leaf segments. Transplastomic clones were identified on a C2 medium by testing leaf segments for resistance to both spectinomycin HCl (200 mg L⁻¹) and streptomycin sulfate (200 mg L⁻¹). Subclones of transplastomic clones were established by rooting spectinomycin-streptomycin resistant shoots on drug-free C1 medium, and were distinguished by capital letters. The subclones were further purified by a second cycle of shoot regeneration on C2 medium containing 400 mg L⁻¹ spectinomycin HCl.

Southern Analysis of Total Cellular DNA

Total leaf cellular DNA was extracted (Mettler 1987), digested with the appropriate restriction enzyme and separated in 0.8% or 1% agarose gels (0.5 μg to 2 μg per lane). After separation, the DNA was transferred to nylon membranes (Amersham) using the PosiBlot transfer apparatus (Stratagene). The blots were probed using Rapid Hybridization Buffer (Amersham) with (³²P)-dCTP labeled probes generated by random priming (Pharmacia). The targeting region in the transformed plants was probed with two plastid DNA fragments containing the 16S rRNA gene: the wild-type HindIII-EcoRI Arabidopsis fragment (P2; GenBank Accession No. AP000423) and the wild-type EcoRI-HincII tobacco plastid DNA fragment (P3, GenBank Accession No. Z00044). Incorporation of aadA in the plastid genome was verified using an NcoI/XbaI fragment (P1 probe) (Sikdar et al. 1998).

Detection of GFP by Fluorescence Microscopy

Subcellular localization of GFP was verified by laser-scanning confocal microscopy (Sarastro 2000 Confocal Image System, Molecular Dynamics, Sunnyvale, Calif.). This system utilizes an argon mixed gas laser with lines at 488 and 568 nm and detector channels. The channels are adjusted for fluorescein and rhodamine images. GFP fluorescence was detected in the FITC channel (488-514 nm). Chlorophyll fluorescence was detected in the TRITC channel (560-580 nm). The images produced by GFP and chlorophyll fluorescence were processed using the Adobe PhotoShop software.

Results

Transformation vectors utilizing tobacco plastid targeting sequences are available (Zoubenko et al. 1994). To minimize potential incompatibility problems, we developed plastid vectors with homologous targeting sequences for the Brassicaceae family. Lesquerella and Arabidopsis belong to this family, therefore we utilized the available Arabidopsis plastid targeting regions. Arabidopsis vector pGS7 has a short targeting segment (Sikdar et al. 1998).

In accordance with the present invention, a new plastid vector for Brassicaceae species has been developed. This plastid vector contains enlarged targeting sequences to facilitate integration. Additionally, HindIII, StuI and XbaI restriction sites have been removed to facilitate DNA manipulations in E. coli. The XbaI site was removed by deleting the terminal 96 nucleotides from the Arabidopsis right targeting region. The HindIII and StuI sites fall within rrn16 (16S rRNA gene). The HindIII and StuI sites in the left targeting region were removed by replacing the Arabidopsis rrn16 sequence with the tobacco rrn16 sequence. The rrn16 coding sequence is highly conserved between tobacco and Arabidopsis; there are only eight point mutations in the 1.3-kb EcoRI-SphI fragment. Therefore, replacement of the Lesquerella rrn16 with the tobacco rrn16 was not expected to impair plastid function. In contrast, sequences outside the rrn16 region are highly divergent between tobacco and Arabidopsis containing several large deletions, insertions and numerous point mutations. The final product, pZS344, has 1.8-kb and 0.9-kb targeting regions and is a backbone for Brassicaceae-specific plastid vectors (FIG. 8A). Plastid vector pZS391B was obtained by ligating aadA16gfp into the HincII site. The aadA16gfp gene encodes aminoglycoside 3′-adenyltransferase translationally fused via a 16-mer linker with the Aequorea victoria green fluorescent protein. The fusion protein confers resistance to spectinomycin and streptomycin when expressed in chloroplasts (Khan and Maliga 1999).

Transplastomic Lesquerella fendleri Clones

Transformation vector pZS391B was introduced into chloroplasts on the surface of tungsten particles by the biolistic process. The leaf sections were incubated on drug-free medium for two days, then transferred to a selective C2 medium containing spectinomycin (400 mg L⁻¹). Lesquerella leaf segments on C2 medium form green shoots on the entire leaf surface. Spectinomycin in the C2 medium in the range of 50 mg L⁻¹ to 400 mg L⁻¹ prevents shoot regeneration and induces formation of non-pigmented (yellow) callus on the leaf sections. Spectinomycin resistant clones were identified as green shoots or green calli (FIG. 9A). From 51 bombarded plates, 110 spectinomycin resistant clones were obtained.

Transplastomic clones expressing aadA16gfp and spontaneous mutants are both resistant to spectinomycin. However, only transplastomic clones are also resistant to streptomycin. Thus, the spectinomycin resistant clones were tested for streptomycin resistance on a C2 medium containing 200 mg L⁻¹ streptomycin and 200 mg L⁻¹ spectinomycin (FIG. 9B). Out of the 110 spectinomycin resistant clones two were identified as transplastomic by cross-resistance to streptomycin. The transplastomic clones were designated Lf-pZS391B-1 and Lf-pZS391B-2.

Results of Southern analysis shown in FIG. 10B suggest a uniform population of transformed plastid genome copies (homoplastomic state) in plants Lf-pZS391B-1 and Lf-pZS391B-2. Plants regenerated from the Lf-pZS391B-1 clone were homoplastomic without further purification. Plants regenerated from the Lf-pZS391B-2 clone initially contained a mixed population of wild type and transformed plastid genome copies. Homoplastomic state in this clone was achieved after two cycles of plant regeneration from leaves on a selective spectinomycin medium. Results shown below were obtained with subclone Lf-pZS391B-2NC.

DNA gel blot analysis was used to test for integration of aadA16gfp and flanking pZS391B plastid targeting sequences into the Lesquerella fendleri plastid genome. In the left and right targeting regions, HindIII, StuI and EcoRI sites distinguish between the Lesquerella genomic sequence and sequences present in vector pZS391B respectively (FIG. 8B). Integration of aadA16gfp was confirmed by probing EcoRI digested DNA with the aadA probe (P1), which hybridizes to a 3.7-kb fragment (FIG. 8C). The segment of plastid genome corresponding to the pZS391B left targeting region in both transgenic lines represent sequences from Lesquerella indicating that aadA16gfp integrated by recombination via sequences directly upstream of the marker gene. This conclusion was drawn from probing EcoRI/HindIII/StuI/HincII digested DNA with the tobacco EcoRI-HincII left targeting region (Probe P3) shown in FIG. 8C.

The transplastomic clones differ with respect to the plastid genome segment corresponding to the right targeting region. Clone Lf-pZS391B-1D carries the Lesquerella sequence as indicated by the presence of the polymorphic EcoRI site. Thus, in this transplastomic clone, the Arabidopsis right targeting region apparently was not incorporated into the Lesquerella plastid genome from vector pZS391B. The second clone, Lf-pZS391B-2NC, lacks the polymorphic Lesquerella EcoRI site. Thus, integration in this clone took place close to the end of the vector right targeting sequence replacing the Lesquerella plastid DNA sequence with the Arabidopsis plastid DNA sequence carried by the transformation vector. These conclusions are based on data obtained from probing EcoRI-digested DNA with the HindIII-EcoRI fragment (Probe P2) shown in FIG. 8C.

Regenerated Lf-pZS391B-1 (subclones D and DD) and wild-type Lesquerella shoots rooted in sterile culture, but did not survive transfer to soil. However, shoots could be grafted onto Brassica napus rootstock, which then flowered and set seed (FIG. 9C). Study of seed transmission of transplastomes was complicated by the lack of wild-type plants with compatible pollen in the greenhouse. However, reciprocal crosses could be made between the transplastomic Lf-pZS391B-1D plant and a spontaneous chloroplast spectinomycin resistant mutant Lf-Spc5 (see below). Both, Lf-pZS391B-1D and Lf-Spc5 plants are resistant to spectinomycin. Chloroplasts of the two lines could be distinguished however, on streptomycin medium: the transplastomic Lf-pZS391B-1D chloroplasts were resistant whereas mutant Lf-Spc5 chloroplasts were sensitive. Seed progeny from a cross using the transplastomic line as female parent segregated for streptomycin resistance (12 greens, 4 whites; 100 mg L⁻¹) indicating that the germline is still heteroplastomic (FIG. 9D). Interestingly, Southern analysis of leaf DNA of the same plants did not reveal heteroplastomy (see above). Seed progeny from the cross with the transplastomic clone as pollen parent yielded only streptomycin sensitive progeny (13 whites). Maternal transmission of streptomycin resistance supports chloroplast localization of the aadA16gfp transgene. Further evidence for chloroplast localization of the transgene was obtained by confocal laser microscopy, which shows GFP encoded by the aadA16gfp gene exclusively in chloroplasts (data not shown).

Plants were also regenerated from the second transplastomic clone, Lf-pZS391B-2N. Three of the subclones that were purified to homoplasmy (NC, NE, NF) grew slowly and had abnormal, bushy morphology. No attempt was made to obtain seed from these plants.

Spontaneous Spectinomycin Resistance Mutants

In the bombarded leaf cultures many spectinomycin resistant clones were obtained which did not carry the aadA16gfp gene. This was not surprising, since spontaneous spectinomycin resistant mutants have been reported in a number of species (Fromm et al. 1987; Svab and Maliga 1991; Kavanagh et al. 1994; Sikdar et al. 1998; Sidorov et al. 1999). Spectinomycin resistance may be due to mutations in the plastid rrn16 gene encoding the 16S rRNA. Mutations conferring spectinomycin resistance often eliminate an AatII recognition sequence localized to a conserved stem structure (Fromm et al. 1987; Svab and Maliga 1991).

DNA was isolated from the leaves of five independent spontaneous spectinomycin resistance mutants (Lf-Spc5, -63, -64, -79, -81) to test for the presence of the conserved AatII site. Digestion with BamHI releases a 3.1-kb rrn16 fragment containing the AatII site. Digestion with both BamHI and AatII yields two fragments if the AatII site is present, which are 0.5-kb and 2.6-kb in size (FIG. 10A). Lack of the AatII site in BamHI/AatII digested DNA of four clones, Lf-Spc5, -63, -64 and 81, is indicated by the presence of the larger 3.1-kb fragment (FIG. 10B). One of the clones, Lf-Scp79 probably contains a mixed population of wild-type and mutant plastid genomes since it has all three fragments.

Seed progeny was obtained from one of the spectinomycin resistant mutants, Lf-Spc5. The selfed seed progeny segregated for spectinomycin resistance when germinated on C1 medium containing spectinomycin (100 mg L⁻¹). Segregation for resistance in the seed progeny indicates that a mixed population of wild-type and mutant plastid genome has been maintained in the germline.

Discussion

Selection of transplastomic clones in tobacco is carried out in a tissue culture system, in which every cell is able to divide and regenerate shoots (Svab et al. 1990; Svab and Maliga 1993). The selective drug suppresses greening and shoot regeneration; thus the transplastomic clones can be readily recognized by formation of green shoots. Identification of transplastomic clones as callus is also feasible but more difficult since, under the conditions employed, sensitive cells also proliferate at a slow rate and the transplastomic cells may be buried in wild-type tissue. In contrast to tobacco, most Arabidopsis leaf cells don't divide on a shoot regeneration medium. Transplastomic clones can not be recovered from these cells, even if their chloroplast genome has been transformed. Transformation protocols in Arabidopsis as described in Examples I-III, employ a two-stage process to circumvent the problem: the first stage involves induction of cell division (callus formation) from every cell, followed by induction of shoots on a selective medium. The efficiency of plastid transformation in this system is low, yielding only one transplastomic clone per 100 bombarded leaf samples (Sikdar et al. 1998). In tobacco, on average, one bombardment yields a transplastomic event. The tissue culture response of Lesquerella leaf cells is similar to that of tobacco leaf cells; in culture virtually every cell is capable of plant regeneration. However, based on the data presented herein, it appears that plastid transformation efficiency in Lesquerella fendleri is comparable to Arabidopsis, yielding one transplastomic clone in 25 samples. Thus, competence for plastid transformation in Lesquerella is not linked to high regeneration capacity.

High frequency of spontaneous spectinomycin resistant (rrn16) mutants indicates that the Lesquerella tissue culture protocol is eminently suitable for the recovery of transplastomic clones by selection for spectinomycin resistance. What could then be the reason for the low efficiency of plastid transformation? Earlier we speculated, that the relatively short targeting sequence may have been the reason for the inefficiency of plastid transformation in Arabidopsis (Sikdar et al. 1998). In the present study, the plastid targeting region of the vector has been enlarged, and now it is comparable to the size of the tobacco vectors (Zoubenko et al. 1994). Thus, the size of the targeting region does not appear to be the reason for the low transformation efficiency in Arabidopsis. Alternative explanation would be relative inefficiency of the recombination system in both Lesquerella and Arabidopsis.

Southern blot analysis of transplastomic line Lf-pZS391B-1D suggested uniformly transformed plastid genomes in the leaves. However, segregation for antibiotic resistance in the seed progeny indicated a heteroplastomic state in the germline. The types of blots shown in FIG. 8C in tobacco would identify plants, which do not segregate wild-type genome copies in the seed progeny (Carrer et al. 1993; Svab and Maliga 1993). Mutant plastids of the Lf-Spc5 clone also appear to be homoplastomic based on Southern probing for the AatII site (FIG. 10B). Still, the seed progeny segregates for spectinomycin resistance. It is likely that homoplastomic plants can be readily obtained in the second seed progeny, as observed in Arabidopsis plastid spectinomycin resistant mutants (data not shown).

Comparative analysis of plastid genomes indicates that while the coding regions are highly conserved, there is a high level of variation in the intergenic regions (Shimada and Sugiura 1991). Is it necessary to construct a plastid vector with homologous targeting sequences for every species? The answer is: probably not, as long as the species are closely related. Potato plastids have been successfully transformed with tobacco plastid targeting sequences (Sidorov et al. 1999) and tobacco plastids have been transformed with Solanum nigrum plastid targeting sequences (Kavanagh et al. 1999). It appears, that efficient plastid transformation with heterologous DNA in higher plants is feasible due to diminished mismatch recombination/repair system mediating integration of foreign DNA via multiple recombination events (Kavanagh et al. 1999). Thus, the practical limit to transformation by heterologous vectors is the lack of ability of the recipient's transcription and translation machinery to properly interpret the heterologous gene expression signals. It is interesting in this regard that the transplastomic clones Lf-pZS391B-1D and Lf-pZS391BD2NC differ with respect to vector sequences replacing the cognate recipient genome segments. Lf-pZS391B-1D does not have any of the RFLPs derived from the vector targeting sequence. In contrast, Lf-pZS391BD2NC plastid DNA carries the Arabidopsis right targeting region RFLP, which lacks the EcoRI site. Therefore, part of the Lesquerella sequence in this transgenic clone has been replaced with the vector right targeting region.

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While certain preferred embodiments of the present invention have been described and specifically exemplified above, it is not intended that the invention be limited to such embodiments. Various modifications may be made to the invention without departing from the scope and spirit thereof as set forth in the following claims. 

1. An improved vector for transforming plastids of higher plants, said vector comprising a targeting segment having first and second targeting sequences for facilitating recombination within the plastid genome within 16S rRNA encoding sequences, each of said first and second targeting sequences flanking at least one transgene of interest, wherein one of said first and second targeting sequence is chimeric, said chimeric targeting sequence having a first portion of a 16S rRNA gene from the plant species targeted for transformation, and a second portion of a 16S rRNA gene from a different plant species.
 2. A vector as claimed in claim 1, wherein said first targeting sequence is chimeric and is obtained from Brassica and Tobacco.
 3. A vector as claimed in claim 1, wherein said second targeting sequence is chimeric and is obtained from Brassica and Tobacco.
 4. A vector as claimed in claim 1, wherein said at least one transgene is a selectable marker gene.
 5. A vector as claimed in claim 1, wherein said at least one transgene is a herbicide resistance gene.
 6. A vector as claimed in claim 1, wherein said at least one transgene is a drought resistance gene.
 7. A vector as claimed in claim 1, said vector comprising the plastid targeting sequence of SEQ ID NO:
 4. 8. A transgenic plant comprising the vector of claim
 1. 9. A transgenic plant comprising the vector of claim
 7. 10. A transgenic Brassica ssp. plant comprising the vector of claim
 1. 11. A transformed plant cell comprising the vector of claim
 1. 12. A transformed plant cell as claimed in claim 11, said cell being selected from the group consisting of cotyledon cells, leaf cells, hypocotyls and root cells.
 13. A vector as claimed in claim 1, wherein said at least one transgene constitutes a monocistronic expression unit.
 14. A vector as claimed in claim 1, wherein said at least one transgene constitutes a polycistronic expression unit comprising a selectable marker gene and a foreign gene of interest, wherein said chimeric targeting sequence is obtained from 16S rRNA encoding sequences from Tobacco and Brassica.
 15. A vector as claimed claim 4, wherein said selectable marker gene encodes a peptide conferring resistance to a selection agent which is selected from the group consisting of kanamycin, streptomycin, and spectinomycin.
 16. A transgenic Brassica plant transformed with the vector of claim
 14. 17. A vector as claimed in claim 1, wherein said plastids are chloroplasts.
 18. An improved vector for transforming plastids of Brassica ssp. and Nicotiana and generation of transplastomic plants therefrom, said vector comprising a targeting segment having first and second targeting sequences for facilitating homologous recombination into 16S rRNA encoding sequences within the plastid genome, each of said first and second targeting sequences flanking at least one transgene of interest, wherein one of said first and second targeting sequences is chimeric, said chimeric targeting sequence being obtained from the 16S rRNA genes of Tobacco and Brassica.
 19. A vector as claimed in claim 18, wherein said first targeting sequence is chimeric.
 20. A vector as claimed in claim 18, wherein said second targeting sequence is chimeric.
 21. A vector as claimed in claim 18, wherein said at least one transgene is a selectable marker gene.
 22. A vector as claimed in claim 18, wherein said at least one transgene is a herbicide resistance gene.
 23. A vector as claimed in claim 18, wherein said at least one trans gene is a drought resistance gene.
 24. A vector for transforming plastids of Brassica ssp. and Nicotiana and generation of transplastomic plants therefrom, said vector comprising a targeting segment having first and second targeting sequences for facilitating homologous recombination within the plastid genome, each of said first and second targeting sequences flanking at least one transgene of interest, wherein one of said first and second targeting sequences being chimeric, said chimeric targeting sequence having a first portion derived from the plant species targeted for transformation, and a second portion derived from a different plant species, said chimeric targeting sequence comprising SEQ ID NO:
 4. 25. A transgenic plant comprising the vector of claim
 18. 26. A transgenic plant comprising the vector of claim
 24. 27. A transgenic Brassica ssp. plant comprising the vector of claim
 18. 28. A transformed plant cell comprising the vector of claim
 18. 29. A transformed plant cell as claimed in claim 28, said cell being selected from the group consisting of cotyledon cells, leaf cells, hypocotyls and root cells.
 30. A vector as claimed in claim 18, wherein said at least one transgene constitutes a monocistronic expression unit.
 31. A vector as claimed in claim 18, wherein said at least one transgene constitutes a polycistronic expression unit comprising a selectable marker gene and a foreign gene of interest.
 32. A vector as claimed in claim 21, wherein said selectable marker gene encodes a peptide conferring resistance to a selection agent which is selected from the group consisting of kanamycin, streptomycin, and spectinomycin.
 33. A transgenic Brassica plant transformed with the vector of claim
 24. 34. A vector as claimed in claim 18, wherein said plastids are chloroplasts. 